Hidden bird migrations revealed by DNA

Every fall, countless songbirds migrate from their breeding grounds in the United States and Canada. Often flying at night to avoid hawks, the animals head south to spend the winter in Mexico and Central America. But exactly where many of them go, and how they get there, has been something of a mystery. Now, a team has shown that analyzing DNA in feathers can provide new details about bird migrations. Although the technique is still in the proof-of-principle stage, it “could be an immensely powerful tool in implementing conservation measures for the most at-risk bird populations with fine-scale precision,” says Jeff Wells of the Boreal Songbird Initiative in Seattle, Washington.

Ornithologists have many ways to track migratory birds. The most common is to put small identification bands on their legs. The trouble is that netters recapture only a tiny fraction of the banded birds. Electronic tracking devices can work well for individual birds, but may not yield insights for an entire population. More recently, researchers have shown that the ratio of isotopes in feathers can provide a rough guide to where a bird has been feeding, because the feather ratios mirror those of food sources. Analysis of mitochondrial and nuclear genes has also offered clues, for example confirming that some birds have geographically distinct breeding populations. But even those techniques couldn’t tease out fine-grained differences in where birds summer and winter. “This is a really big issue,” because conservation groups need to know where to spend their resources to best effect, says Robert Fleischer, a geneticist at the Smithsonian Conservation Biology Institute in Washington D.C.

In a bid to get more detail, the new study used genomic markers—called single nucleotide polymorphisms (SNPs)—to distinguish populations. The DNA came from a remarkable collection of more than 180,000 feathers from about 50 species stored in freezers at the University of California, Los Angeles (UCLA). Ecologist Thomas Smith has been gathering the feather samples for more than 2 decades; when other researchers band birds, they pull a tail feather and mail it to Smith. Tissue at the base of the feather contains enough DNA for researchers to analyze.

The researchers focused on a perky, black-capped yellow bird called the Wilson's warbler (Cardellina pusilla). Previous genetic studies had shown that the warblers have separate breeding populations in the eastern and western United States. But researchers suspected that there are several subpopulations, such as in the Sierra Nevada and Colorado Plateau. To make matters more complex, each might have its own wintering grounds. To see if they could detect those linkages, they first examined DNA from 22 birds captured in five regions of the United States, sequencing 150,000 regions of their genomes. From a pool of a half-million SNPs, they chose 96 that could best distinguish the birds. Then, they compared those SNPs with those taken from a second set of 1626 feathers from 68 locations across North and Central America.

The results, posted on 8 August in a preprint on bioRxiv, showed six genetically distinct groups of Wilson’s warbler. The study confirmed that birds breeding along the California coast spend the winter in southern Baja, for example, and warblers in the eastern United States head for the Yucatan, Belize, and Costa Rica. But the SNPs also provided the first strong evidence that warblers in the southern Rocky Mountains and the Colorado Plateau overwinter in El Salvador.

The researchers also got the first clear look at migration timing. Team member Kristina Paxton of the University of Hawaii, Hilo, spent 2 months catching warblers in 2008 and again in 2009 as they passed through a stopover site on the Lower Colorado River in Arizona. DNA from the feathers showed that birds headed to California flew through first, followed by those going to the Pacific Northwest, the Sierra Nevada, and finally Alaska. In the future, researchers might be able to tell when at-risk populations of other species pass through.

The genomic tools provide “resolution of populations that we’ve never seen before,” says Kristen Ruegg, an evolutionary geneticist at UCLA, one of the study’s authors. Now, Ruegg and colleagues would like to expand the analysis to other migratory birds, including endangered species, if they can get funding. Douglas Robinson, an ecologist at Oregon State University, Corvallis, calls the approach “probably the wave of the future” for determining geographic connections on a regional scale, but he thinks that more detail will be needed to make a difference in conservation.

The paper is in review at Molecular Ecology, and Ruegg will discuss the work in a webinar, sponsored by the U.S. Fish and Wildlife Service, on Thursday at 2 p.m. EDT.